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The bill was requested by the Canterbury Regional Council, is specific to it, and was in the name of Tino Tirikatene, the MP for Te Tai Tonga.
A group of Ngāi Tahu including 83-year-old Sir Tipene O'Regan, the 2022 New Zealander of the Year, watched the third reading debate from the galleries above.
One Labour speaker, Tangi Utikere, apologised to Ngāi Tahu for some of the speeches that had been made by Opposition MPs, an apology which National MP Gerry Brownlee objected to.
Brownlee said the whole purpose of the chamber was to reflect all points of view and apologies were not required.
Tirikatene described the bill, the Canterbury Regional Council (Ngai Tahu Representation) Amendment Bill was "about the evolution of our treaty partnership and representation of Māori, of iwi at the local government level".
"Ngāi Tahu are entitled to this representation because that is the promise of the Treaty of Waitangi and this is a modern-day expression of that promise."
The two Ngāi Tahu members of council will be appointed after the 2022 elections, and will be in addition to 14 elected councillors.
National's Paul Goldsmith said National would repeal the law if it became the Government because it did not uphold equal voting rights for all New Zealanders and did not provide electoral accountability. He questioned the mandate for the bill.
"It is our view on this side of the House that the Treaty of Waitangi does not trump democracy and the country has not decided that," he said.
It was a divisive bill that was pitting one group of New Zealanders against others.
"Ngāi Tahu get to appoint those two councillors forever and a day. They cannot be thrown out. There is no direct accountability. It astounds me that I'm having to make this argument."
Goldsmith rejected a suggestion that the bill had its roots in a similar move National had made in Government in 2010 when it replaced the Canterbury Regional Council with commissioners, including two Ngai Tahu commissioners.
"It will set a precedent. There is no question about that across local government. I can't how you could say this is modern expression of the treaty but it only applies to Canterbury.
"I am sure there will be many other councils to which this logic will flow to, and then potentially to central government."
Labour MP Tamati Coffey read out part of the Crown's apology to Ngāi Tahu written into its Treaty of Waitangi settlement bill in 1997.
Labour list MP Tamati Coffey read out part of the Crown's apology to Ngāi Tahu in its 1997 settlement legislation, with reference to its desire to enter a new age of co-operation.
"I apologise that it has taken this long. And I apologise that you have had to go through this process."
But he said Ngāi Tahu had opened the door to other iwi.
"All of those iwi out there that are struggling with how representation works for them and their rohe, I hope that they are understanding that this is a potential pathway.
Green MP Eugenie Sage said no other group would be materially disadvantaged by the bill.
Labour Christchurch Central MP Duncan Webb, a former law lecturer, said Ngāi Tahu had been recognised as having special rights because of significant historical wrongs and grievances that needed to be addressed.
"This step today is part of that story that continues," he said.
"This is a genuine partnership with our treaty partners, a partnership which must and will endure."
Brownlee said the bill was the result of a "very bad process".
He said it was essentially a "backdoor process" and if the Government believed it was good for Ngāi Tahu, why wasn't it offering the same to other iwi.
He said the co-governance arrangements put in place by the former National government had been appropriate and were not central to the primary purpose of either central or local government.
He believed there would be more of them.
His objection was that a proper process had not been followed. He also regretted an apparent breakdown in relationship between National and Ngāi Tahu.
"I think there is perhaps not a deep enough understanding on either part about where either party might be coming from."
-By Audrey Young